Does PhaseByTransmission remove calls?

apolyakapolyak State College, PA, USAMember

When I run VariantsToTable (using -raw option) on vcf file and get more output SNPs in a table, than when I do the same thing on the VCF calls output by PhaseByTransmission.

I feel as though PhaseByTransmission filters out calls? I'm trying to keep all the SNPs I have, so I can filter manually last.

Answers

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @apolyak
    Hi,

    Can you tell me the exact command you ran for VariantsToTable? How are you comparing the numbers of SNPs? Can you post some records of sites that are missing? Also, were the VCFs generated by GATK?

    Thanks,
    Sheila

  • apolyakapolyak State College, PA, USAMember

    So, I think I found what PhaseByTransmission is removing. I have two VCF files (one from freebayes, and one from GATK) which I combind using CombineVariants. Now, I used the --setKey "dataset" to output a column that says where the record came from. For some records, the term in the dataset feild included the term "filterIn". Records with "filterIn" seem to have been removed.

  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin

    @apolyak
    Hi,

    I am happy you figured out what was causing the issue.

    -Sheila

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